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https://www.readbyqxmd.com/read/28821952/genome-wide-association-study-and-gene-set-analysis-for-understanding-candidate-genes-involved-in-salt-tolerance-at-the-rice-seedling-stage
#1
Jie Yu, Weiguo Zao, Qiang He, Tae-Sung Kim, Yong-Jin Park
Salt is the major factor limiting crop productivity in saline soils and is controlled by various genes. The development of salt-tolerant rice through molecular breeding methods is important to meet the needs of rice breeding. We used 295 accessions to perform a genome-wide association study (GWAS) of salt tolerance-related phenotypes in rice at the seedling stage and obtained 93 candidate genes with high association peaks across six phenotypes. We constructed a protein interaction network using the candidate genes identified here, and 33 genes were associated...
August 18, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28821913/molecular-insights-into-the-origin-of-the-brown-rust-resistance-gene-bru1-among-saccharum-species
#2
Heng-Bo Wang, Ping-Hua Chen, Yan-Qing Yang, Angelique D'Hont, Yun-Hai Lu
Analysis of 387 sugarcane clones using Bru 1 diagnostic markers revealed two possible sources of Bru 1 in Chinese cultivars: one from Saccharum spontaneum and another from Saccharum robustum of New Guinea. Sugarcane brown rust (SBR) is an important fungal disease in many sugarcane production areas around the world, and can cause considerable yield losses in susceptible sugarcane cultivars. One major SBR resistance gene, named Bru1, initially identified from cultivar R570, was shown to be a major SBR resistance source in most of the sugarcane producing areas of the world...
August 18, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28821241/genetic-diversity-and-virulence-potential-of-clinical-and-environmental-aeromonas-spp-isolates-from-a-diarrhea-outbreak
#3
Lívia Christina Alves da Silva, Tereza Cristina Leal-Balbino, Beatriz Souza Toscano de Melo, Carina Lucena Mendes-Marques, Antonio Mauro Rezende, Alzira Maria Paiva de Almeida, Nilma Cintra Leal
BACKGROUND: Aeromonas spp. are gram-negative bacteria that can cause a variety of infections in both humans and animals and play a controversial role in diarrhea outbreaks. Our aim was to identify clinical and environmental Aeromonas isolates associated with a cholera outbreak in a northeast county of Brazil at the species level. We also aimed to determine the genetic structure of the bacterial population and the virulence potential of the Aeromonas isolates. METHODS AND RESULTS: Analysis based on concatenated sequences of the 16S rRNA and gyrB genes suggested the classification of the 119 isolates studied into the following species: A...
August 18, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28818649/sequence-analysis-of-mtdna-coi-barcode-region-revealed-three-haplotypes-within-culex-pipiens-assemblage
#4
Mona Koosha, Mohammad Ali Oshaghi, Mohammad Mehdi Sedaghat, Hassan Vatandoost, Shahyad Azari-Hamidian, Mohammad Reza Abai, Ahmad Ali Hanafi-Bojd, Fatemeh Mohtarami
Members of the Culex (Culex) pipiens assemblage are known vectors of deadly encephalitides, periodic filariasis, and West Nile virus throughout the world. However, members of this assemblage are morphologically indistinguishable or hard to distinguish and play distinct roles in transmission of the diseases. The current study aimed to provide further evidence on utility of the two most popular nuclear (ITS2-rDNA) and mitochondrial (COI barcode region) genetic markers to identify members of the assemblage. Culex pipiens assemblage specimens from different climate zones of Iran were collected and identified to species level based on morphological characteristics...
August 14, 2017: Experimental Parasitology
https://www.readbyqxmd.com/read/28817824/parametric-linkage-analysis-identifies-five-novel-genome-wide-significant-loci-for-familial-lung-cancer
#5
Anthony M Musolf, Claire L Simpson, Mariza de Andrade, Diptasri Mandal, Colette Gaba, Ping Yang, Yafang Li, Ming You, Elena Y Kupert, Marshall W Anderson, Ann G Schwartz, Susan M Pinney, Christopher I Amos, Joan E Bailey-Wilson
OBJECTIVE: One of four American cancer patients dies of lung cancer. Environmental factors such as tobacco smoking are known to affect lung cancer risk. However, there is a genetic factor to lung cancer risk as well. Here, we perform parametric linkage analysis on family-based genotype data in an effort to find genetic loci linked to the disease. METHODS: 197 individuals from families with a high-risk history of lung cancer were recruited and genotyped using an Illumina array...
August 18, 2017: Human Heredity
https://www.readbyqxmd.com/read/28816920/similar-metabolic-innate-immunity-and-adipokine-profiles-in-adult-and-pediatric-sepsis-versus-systemic-inflammatory-response-syndrome-a-pilot-study
#6
Theonymfi Tavladaki, Anna Maria Spanaki, Helen Dimitriou, Efmorfia Kondili, Christianna Choulaki, Dimitris Georgopoulos, George Briassoulis
OBJECTIVES: To examine whether the septic profiles of heat shock protein 72, heat shock protein 90α, resistin, adiponectin, oxygen consumption, CO2 production, energy expenditure, and metabolic pattern, along with illness severity, nutritional, and inflammatory indices, differ between adult and pediatric patients compared with systemic inflammatory response syndrome and healthy controls. To evaluate whether these biomolecules may discriminate sepsis from systemic inflammatory response syndrome in adult and pediatric patients...
August 12, 2017: Pediatric Critical Care Medicine
https://www.readbyqxmd.com/read/28814372/association-of-cyp19a1-gene-polymorphisms-with-anoestrus-in-water-buffaloes
#7
Khairy M El-Bayomi, Ayman A Saleh, Ashraf Awad, Mahmoud S El-Tarabany, Hadeel S El-Qaliouby, Mohamed Afifi, Shymaa El-Komy, Walaa M Essawi, Essam A Almadaly, Mohammed A El-Magd
Cytochrome P450 aromatase (encoded by the CYP19A1 gene) regulates oestrogen biosynthesis and so plays an essential role in female fertility. We investigated the genetic association of CYP19A1 with the risk of anoestrus in Egyptian water buffaloes. A total of 651 animals (326 anoestrous and 325 cycling) were used in this case-control study. Using single-strand conformation polymorphisms and sequencing, four single nucleotide polymorphisms (SNPs) were detected; c.-135T>C SNP in the 5'UTR and three non-synonymous SNPs: c...
August 17, 2017: Reproduction, Fertility, and Development
https://www.readbyqxmd.com/read/28813580/genetic-association-of-the-parl-abcc5-htr3d-htr3c-locus-with-primary-angle-closure-glaucoma-in-chinese
#8
Fang Yao Tang, Li Ma, Pancy O S Tam, Chi Pui Pang, Clement C Y Tham, Li Jia Chen
Purpose: This study evaluates the associations of haplotype-tagging single nucleotide polymorphisms (SNPs) in the PARL-ABCC5-HTR3D-HTR3C region with primary angle closure glaucoma (PACG), with a view to identify the responsible SNP in this region. Methods: Thirty SNPs from the PARL-ABCC5-HTR3D-HTR3C region were genotyped in a Hong Kong Chinese cohort of 422 PACG patients and 400 control subjects, using TaqMan SNP genotyping assays. Single marker and haplotype-based association analyses were performed...
August 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28813463/genetic-diversity-of-bemisia-tabaci-species-colonizing-cassava-in-central-african-republic-characterized-by-analysis-of-cytochrome-c-oxidase-subunit-i
#9
Brice Kette Tocko-Marabena, Semballa Silla, Christophe Simiand, Innocent Zinga, James Legg, Bernard Reynaud, Helene Delatte
After 2007, upsurges of whiteflies on cassava plants and high incidences of cassava diseases were observed in Central African Republic. This recent upsurge in the abundance of Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) was directly linked to serious damage to cassava crops resulting from spread of whitefly-borne cassava mosaic geminiviruses (CMGs). There is currently very little information describing whitefly populations on cassava and associated crops in Central African Republic. The current study aimed to address this gap, and to determine whether the increasing damage associated with B...
2017: PloS One
https://www.readbyqxmd.com/read/28812414/adipokine-genes-and-radiographic-hand-osteoarthritis-in-finnish-women-a-cross-sectional-study
#10
S Hämäläinen, S Solovieva, T Vehmas, A Hirvonen, P Leino-Arjas
OBJECTIVES: Available evidence suggests that genetic factors and overweight play major roles in the aetiology of osteoarthritis (OA). We analysed the association of 18 single-nucleotide polymorphisms (SNPs) from nine adipokine and adipokine receptor genes (LEP, LEPR, ADIPOQ, RETN, NAMPT, SERPINA12, ITLN1, RARRES2, and APLN) with radiographic hand OA. METHOD: The study design was cross-sectional. Bilateral hand radiographs of 542 occupationally active Finnish female dentists and teachers aged 45-63 years were examined and classified for the presence of hand OA using reference images...
August 16, 2017: Scandinavian Journal of Rheumatology
https://www.readbyqxmd.com/read/28811688/genetic-variation-in-cd166-gene-and-its-association-with-bladder-cancer-risk-in-north-indian-population
#11
Archana Verma, Rakesh Kapoor, Rama Devi Mittal
Adhesion molecules play a key role in cancer progression and tumorigenesis. Genetic polymorphism of adhesion molecules may alter the normal functioning thereby leading to bladder cancer susceptibility. Hence we aimed to evaluate three SNPs of CD166 gene (CD166rs6437585 C/T, CD166rs10511244 C/T, and CD166rs1157 A/G) in bladder cancer patients and normal controls of North Indian population. A total of 270 healthy controls and 240 confirmed bladder cancer patients were recruited for this study. Three SNPs of CD166 gene viz...
July 2017: Indian Journal of Clinical Biochemistry: IJCB
https://www.readbyqxmd.com/read/28809744/effect-of-vitamin-d-serum-levels-and-gc-gene-polymorphisms-in-liver-fibrosis-due-to-chronic-hepatitis-c
#12
Laura A Azevedo, Ursula Matte, Themis R Silveira, Jacqueline W Bonfanti, Juliana P Bruch, Mário R Álvares-da-Silva
INTRODUCTION AND AIM: Vitamin D has been associated with chronic liver diseases and low vitamin levels may contribute to progression of chronic hepatitis C. The aim of this study was to evaluate the influence of vitamin D serum levels and GC gene polymorphisms in the severity of liver fibrosis in patients with chronic hepatitis C genotype 1. MATERIAL AND METHODS: Cross-sectional study that enrolled 132 adult patients with chronic hepatitis C genotype 1 attended at the outpatient Clinic of Gastroenterology Division at Hospital de Clínicas de Porto Alegre...
August 8, 2017: Annals of Hepatology
https://www.readbyqxmd.com/read/28804492/population-genetic-differentiation-and-taxonomy-of-three-closely-related-species-of-saxifraga-saxifragaceae-from-southern-tibet-and-the-hengduan-mountains
#13
Qing-Bo Gao, Yan Li, Zhuo-Ma Gengji, Richard J Gornall, Jiu-Li Wang, Hai-Rui Liu, Liu-Kun Jia, Shi-Long Chen
The effects of rapid, recent uplift of the Hengduan Mountains on evolution and diversification of young floristic lineages still remain unclear. Here, we investigate diversification of three closely related Saxifraga species with a distribution restricted to the Hengduan Mountains (HM) and southern Tibet, and comment on their taxonomy based on molecular evidence. Three chloroplast DNA fragments (rbcL, trnL-F, trnS-G) and the nuclear ribosomal DNA internal transcribed spacer (ITS) were employed to study genetic structure across 104 individuals from 12 populations of Saxifraga umbellulata, S...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28803225/carboxylesterase-1a2-encoding-gene-with-increased-transcription-and-potential-rapid-drug-metabolism-in-asian-populations
#14
Henrik Berg Rasmussen, Majbritt Busk Madsen, Yassine Kamal Lyauk, Peter Riis Hansen, Timothy Hughes
The carboxylesterase 1 gene (CES1) encodes a hydrolase implicated in the metabolism of commonly used drugs. CES1A2, a hybrid of CES1 and a CES1-like pseudogene, has a promoter that is weak in most individuals. However, some individuals harbor a promoter haplotype of this gene with two overlapping Sp1 sites that confer significantly increased transcription potentially leading to rapid drug metabolism. This CES1A2 haplotype has previously been reported to be common among Asians. Using polymerase chain reaction followed by sequencing, the present study examined variation in the promoter and 5' untranslated region of CES1A2 in 120 Han Chinese and 120 Japanese people enrolled in the 1000 Genomes Project...
August 14, 2017: Drug Metabolism and Personalized Therapy
https://www.readbyqxmd.com/read/28803020/a-missense-mutation-in-pfas-phosphoribosylformylglycinamidine-synthase-is-likely-causal-for-embryonic-lethality-associated-with-the-mh1-haplotype-in-montb%C3%A3-liarde-dairy-cattle
#15
Pauline Michot, Sébastien Fritz, Anne Barbat, Mekki Boussaha, Marie-Christine Deloche, Cécile Grohs, Chris Hoze, Laurène Le Berre, Daniel Le Bourhis, Olivier Desnoes, Pascal Salvetti, Laurent Schibler, Didier Boichard, Aurélien Capitan
A candidate mutation in the sex hormone binding globulin gene was proposed in 2013 to be responsible for the MH1 recessive embryonic lethal locus segregating in the Montbéliarde breed. In this follow-up study, we excluded this candidate variant because healthy homozygous carriers were observed in large-scale genotyping data generated in the framework of the genomic selection program. We fine mapped the MH1 locus in a 702-kb interval and analyzed genome sequence data from the 1,000 bull genomes project and 54 Montbéliarde bulls (including 14 carriers and 40 noncarriers)...
August 9, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28802359/transmission-analysis-of-tgfb1-gene-polymorphisms-in-non-syndromic-cleft-lip-with-or-without-cleft-palate
#16
Ginila T Raju, Bhaskar V K S Lakkakula, Jyotsna Murthy, Munirajan Arasambattu Kannan, Solomon F D Paul
OBJECTIVES: Transforming growth factor beta1 (TGF-β1) plays a significant role in craniofacial development. Previous linkage studies reported that the TGF-β1-locus at 19q13.1 harbour predisposing genes for non-syndromic oral clefts. In the present study case parents triads were evaluated to find the transmission effects of genetic variants in TGF- β1 towards non-syndromic cleft lip or palate (NSCL/P). METHODS: Using allelic discrimination method148 families (case-parent triads) were assessed for single nucleotide polymorphisms (SNPs) in TGF-β1 gene...
September 2017: International Journal of Pediatric Otorhinolaryngology
https://www.readbyqxmd.com/read/28801681/nrf1-and-zscan10-bind-to-the-promoter-region-of-the-six1-gene-and-their-effects-body-measurements-in-qinchuan-cattle
#17
Da-Wei Wei, Lin-Sheng Gui, Sayed Haidar Abbas Raza, Song Zhang, Rajwali Khan, Li Wang, Hong-Fang Guo, Lin-Sen Zan
The SIX1 homeobox gene belongs to the six homeodomain family and is widely thought to play a principal role in mediating of skeletal muscle development. In the present study, we determined that the bovine SIX1 gene was highly expressed in the longissimus thoracis and physiologically immature individuals. DNA sequencing of 428 individual Qinchuan cattle identified nine single nucleotide polymorphisms (SNPs) in the promoter region of the SIX1 gene. Using a series of 5' deletion promoter plasmid luciferase reporter assays and 5'-rapid amplification of cDNA end analysis (RACE), two of these SNPs were found to be located in the proximal minimal promoter region -216/-28 relative to the transcriptional start site (TSS)...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28800731/the-analysis-of-apol1-genetic-variation-and-haplotype-diversity-provided-by-1000-genomes-project
#18
Ting Peng, Li Wang, Guisen Li
BACKGROUND: The APOL1 gene variants has been shown to be associated with an increased risk of multiple kinds of diseases, particularly in African Americans, but not in Caucasians and Asians. In this study, we explored the single nucleotide polymorphism (SNP) and haplotype diversity of APOL1 gene in different races provided by 1000 Genomes project. METHODS: Variants of APOL1 gene in 1000 Genome Project were obtained and SNPs located in the regulatory region or coding region were selected for genetic variation analysis...
August 11, 2017: BMC Nephrology
https://www.readbyqxmd.com/read/28798757/establishing-the-bases-for-introducing-the-unexplored-portuguese-common-bean-germplasm-into-the-breeding-world
#19
Susana T Leitão, Marco Dinis, Maria M Veloso, Zlatko Šatović, Maria C Vaz Patto
Common bean (Phaseolus vulgaris L.) is among the most important grain legumes for human consumption worldwide. Portugal has a potentially promising common bean germplasm, resulting from more than five centuries of natural adaptation and farmers' selection. Nevertheless, limited characterization of this resource hampers its exploitation by breeding programs. To support a more efficient conservation of the national bean germplasm and promote its use in crop improvement, we performed, for the first time, a simultaneous molecular marker (21 microsatellites and a DNA marker for phaseolin-type diversity analysis) and seed and plant morphological characterization (14 traits) of 175 accessions from Portuguese mainland and islands traditional bean-growing regions...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28798540/growth-differentiation-factor-15-may-predict-mortality-of-peripheral-and-coronary-artery-diseases-and-correlate-with-their-risk-factors
#20
Lung-An Hsu, Semon Wu, Jyh-Ming Jimmy Juang, Fu-Tien Chiang, Ming-Sheng Teng, Jeng-Feng Lin, Hsuan-Li Huang, Yu-Lin Ko
Plasma GDF15 concentrations were measured in 612 Taiwanese individuals without overt systemic disease. Clinical parameters, GDF15 genetic variants, and 22 biomarker levels were analyzed. We further enrolled 86 patients with PAD and 481 patients with CAD, who received endovascular intervention and coronary angiography, respectively, to examine the role of GDF15 level in predicting all-cause mortality. Significant associations were found between GDF15 genotypes/haplotypes and GDF15 levels. The circulating GDF15 level was positively associated with age, smoking, hypertension, and diabetes mellitus as well as circulating levels of lipocalin 2 and various biomarkers of inflammation and oxidative stress...
2017: Mediators of Inflammation
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